The Sixth Annual Paris C. Kanellakis Memorial Lecture

"Whole Genome Sequencing and Imaging-Based Systems Biology"

Eugene W. Myers, Howard Hughes Medical Institute

Thursday, February 15, 2007 at 4:00 P.M.

Room 368 (CIT 3rd Floor)

The whole-genome shotgun sequencing method with paired end-reads has proven rapid and economical, producing high-quality reconstructions of Drosophila (2000), Human (2001) and Mouse (2001), in quick succession. We discuss the overall algorithmic strategy, and the results one can expect by comparing the whole genome assembly of Drosophila against the finished sequence.

Because the finishing phase of genome assembly is an order of magnitude more expensive then the shotgun phase, most genomes being sequenced today will never be finished. This makes the goal of building better whole genome assemblers more important than ever. We present a new string-graph approach and several other improvements, giving preliminary results. We also discuss recent advances in sequencing technology.

Much hope has been placed on comparative genomics as the easiest route to near-perfect annotation of genes and regulatory elements. We discuss the problem of gene finding and raise the issue that algorithms to date are not performing at the expected level.

This leads us to conclude with a segment on the possibility of a program of high-throughput in-situ image analysis in D. melanogaster and C. elegans embryos. We describe preliminary results on limited data sets and extrapolate on what we might be able to infer from such data. We speculate that this may be the best way to understand the developmental cis-regulatory network of the genome from a systems perspective.

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This lecture series honors Paris Kanellakis, a distinguished computer scientist who was an esteemed and beloved member of the Brown Computer Science department. Paris joined the Computer Science Department in 1981 and became a full professor in 1990. His research area was theoretical computer science, with emphasis on the principles of database systems, logic in computer science, the principles of distributed computing and combinatorial optimization. He died in an airplane crash on December 20, 1995, along with his wife, Maria Teresa Otoya, and their two young children, Alexandra and Stephanos Kanellakis.